Kaitlyn K. Spees

In vivo intercellular CRISPR screens using viral proximity barcoding reveal regulators of tumor-immune interactions

This study introduces match-seq, a method to trace cell-cell interactions in vivo using CRISPR screens, revealing genetic regulators of tumor-immune interactions.

Efficient exploration of sequence space enables rapid generation of functional genome editors

The paper generates functional genome editors by combining deep mutational scanning, structural analysis, and evolutionary mining with a generative protein language model.

A microproteome screen identifies immunomodulatory bacterial microproteins encoded in expanded gene arrays in Leptotrichia

The paper identifies immunomodulatory bacterial microproteins from Leptotrichia using a microproteome screen and shows they influence macrophage polarization.

An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates

The paper uses an image-based CRISPR screen to show splicing regulates HP1α condensates through RNA-chromatin interactions, affecting heterochromatin organization and stress response genes.

RIG-I-dependent tumor-intrinsic type I interferon signaling restricts growth in breast cancer 3D culture

This study identifies type I interferon signaling as a tumor-intrinsic suppressor of proliferation in 3D breast cancer spheroids through RIG-I-mediated sensing of cytosolic RNA.

Development of compact transcriptional effectors using high-throughput measurements in diverse contexts

The paper develops HT-recruit to measure transcriptional effector function across contexts and identifies context-dependent effectors for CRISPR-based transcription control.

Prediction and design of transcriptional repressor domains with large-scale mutational scans and deep learning

The paper predicts and designs transcriptional repressor domains using mutational scans and a deep learning model called TENet, identifying functional variants and enabling synthetic design.

High-throughput functional characterization of combinations of transcriptional activators and repressors

The paper measures how combinations of transcriptional activators and repressors affect gene expression and uses this to create a tunable synthetic transcription factor.

Large-scale mapping and systematic mutagenesis of human transcriptional effector domains

The paper systematically maps and characterizes transcriptional effector domains in human chromatin regulators and transcription factors, identifying new activation and repression domains and their functional features.

A genome-wide almanac of co-essential modules assigns function to uncharacterized genes

This paper develops a statistical method to identify gene co-essentiality, creating a genome-wide functional module almanac that predicts functions for 102 uncharacterized genes and validates key findings.

High-throughput discovery and characterization of human transcriptional effectors

The paper develops HT-recruit, a high-throughput assay to identify transcriptional effectors in human proteins, finding repressor function correlates with evolutionary age and discovering new activator domains.

Identification and mitigation of pervasive off-target activity in CRISPR-Cas9 screens for essential non-coding elements

The paper identifies off-target effects in CRISPR-Cas9 screens for non-coding elements and shows that strict filtering with specificity scores improves the identification of essential regulatory regions.

Genetic architecture drives seasonal onset of hibernation in the 13-lined ground squirrel

The paper identifies genetic loci associated with the seasonal onset of hibernation in 13-lined ground squirrels, finding high heritability and significant associations with genes involved in energy homeostasis and insulin signaling.